Interpretive Summary: Soybean oil with reduced palmitate content will be a healthier alternative to the normal fatty acid profile of commodity type soybeans. A novel point mutation identified in the germplam line C1726 causes a significant reduction in palmitic acid content. This mutation is a single nucleotide polymorphism in the GmKASIIIA locus that disrupts the donor splice site recognition between exon one and intron one producing a truncated KASIIIA protein. Interestingly, it was demonstrated that this mutation causes a significant enhancement in the expression of this gene. However, the protein produced appears to be a non functional enzyme. To the best of our knowledge, this is the first instance of an enhanced expression motif reported in a soybean gene involved in the fatty acids pathway. This mutation caused a significant reduction in 16:0, 18:0 and oil content but did not have a significant impact on seed yield.

Technical Abstract:
Soybean oil with reduced palmitic acid content is desirable to reduce the risks of coronary diseases and; breast, colon, and prostate cancer incidence associated with consumption of this fatty acid. The objectives of this study were: to identify the genomic location of the reduced palmitate fap1 mutation, determine its the molecular basis, estimate the amount of phenotypic variation in the 16:0, 18:0, 18:1, 18:2 and 18:3 composition that is explained by this locus, determine if there are epistatic interactions between the fap1 and fapnc loci and, determine if the fap1 mutation has pleiotropic effects on seed yield, oil and protein content in three soybean populations grown in multiple environments. One of the populations consisted of 712 F5-derived lines, providing excellent precision for estimation of the genetic parameters. This study detected two major QTL for 16:0 content located in Chromosome 5 (GmFATB1a, fapnc) and Chromosome 9 near BARCSOYSSR_09_1707 that explained with their interaction 66 to 94 % of the variation in 16:0 content in the three populations. Sequencing results of a putative candidate gene, GmKASIIIA, revealed a single unique polymorphism in the germplasm line ‘C1726’, which was predicted to disrupt the donor splice site recognition between exon one and intron one and produce a truncated KASIIIA protein. In addition, this G to A change also created the GATCTG motif that enhanced gene expression of the mutated GmKASIIIA gene in this study. Lines homozygous for the GmKASIIIA mutation (fap1) had a significant reduction in 16:0, 18:0, and oil content and an increase in unsaturated fatty acids content in these three populations. There were significant epistatic interactions between GmKASIIIA (fap1) and fapnc for 16:0 and oil contents, and seed yield in 2 populations. In conclusion, the fap1 phenotype is caused by a single unique SNP in the GmKASIIIA gene.